Starting phenix.real_space_refine
on Fri Jul 25 13:51:08 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/9dka_46949/07_2025/9dka_46949_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dka_46949/07_2025/9dka_46949.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dka_46949/07_2025/9dka_46949.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dka_46949/07_2025/9dka_46949.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dka_46949/07_2025/9dka_46949_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dka_46949/07_2025/9dka_46949_trim.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.015
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Br      2      7.06       5
     S      26      5.16       5
     C    2501      2.51       5
     N     656      2.21       5
     O     662      1.98       5
     H    3879      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7726
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 517, 7704
          Classifications: {'peptide': 517}
          Link IDs: {'PTRANS': 30, 'TRANS': 486}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 82
          Unresolved non-hydrogen dihedrals: 48
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 30
    Chain: "A"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Unusual residues: {'R75': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.11, per 1000 atoms: 0.53
  Number of scatterers: 7726
  At special positions: 0
  Unit cell: (79.515, 90.63, 84.645, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Br      2     34.99
     S      26     16.00
     O     662      8.00
     N     656      7.00
     C    2501      6.00
     H    3879      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  49 " - pdb=" SG  CYS A 116 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  88 " - pdb=" SG  CYS A 139 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.91
  Conformation dependent library (CDL) restraints added in 774.4 milliseconds
  

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  940

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 3 sheets defined
      80.9% alpha, 1.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 11
      removed outlier: 3.924A  pdb=" N   LEU A   6 " --> pdb=" O   ALA A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 37
      Proline residue:  A  27  - end of helix
      removed outlier: 4.185A  pdb=" N   TRP A  30 " --> pdb=" O   VAL A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 42
    Processing helix  chain 'A' and resid 51 through 56
    Processing helix  chain 'A' and resid 56 through 63
      removed outlier: 3.757A  pdb=" N   VAL A  63 " --> pdb=" O   ALA A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 74
      removed outlier: 3.820A  pdb=" N   ALA A  74 " --> pdb=" O   GLU A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 111
      No H-bonds generated for 'chain 'A' and resid 109 through 111'
    Processing helix  chain 'A' and resid 130 through 136
    Processing helix  chain 'A' and resid 138 through 142
    Processing helix  chain 'A' and resid 143 through 171
      removed outlier: 3.588A  pdb=" N   ILE A 156 " --> pdb=" O   TYR A 152 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU A 157 " --> pdb=" O   LEU A 153 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ALA A 161 " --> pdb=" O   LEU A 157 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLY A 164 " --> pdb=" O   ALA A 160 " (cutoff:3.500A)
      Proline residue:  A 165  - end of helix
      removed outlier: 3.578A  pdb=" N   ARG A 169 " --> pdb=" O   PRO A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 192
      removed outlier: 3.652A  pdb=" N   PHE A 192 " --> pdb=" O   THR A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 224
      removed outlier: 3.621A  pdb=" N   TRP A 224 " --> pdb=" O   LEU A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 253
      removed outlier: 3.821A  pdb=" N   THR A 235 " --> pdb=" O   PRO A 231 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   HIS A 245 " --> pdb=" O   PHE A 241 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   VAL A 246 " --> pdb=" O   SER A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 267
    Processing helix  chain 'A' and resid 267 through 276
      removed outlier: 4.138A  pdb=" N   LEU A 271 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 290
    Processing helix  chain 'A' and resid 291 through 307
    Processing helix  chain 'A' and resid 308 through 315
      removed outlier: 3.641A  pdb=" N   LEU A 315 " --> pdb=" O   VAL A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 324
    Processing helix  chain 'A' and resid 324 through 330
      removed outlier: 3.911A  pdb=" N   VAL A 330 " --> pdb=" O   GLU A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 343
      removed outlier: 3.810A  pdb=" N   THR A 343 " --> pdb=" O   THR A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 368
    Processing helix  chain 'A' and resid 371 through 375
    Processing helix  chain 'A' and resid 377 through 403
      removed outlier: 3.974A  pdb=" N   LEU A 381 " --> pdb=" O   ASN A 377 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLY A 386 " --> pdb=" O   GLN A 382 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ILE A 390 " --> pdb=" O   GLY A 386 " (cutoff:3.500A)
      Proline residue:  A 391  - end of helix
      removed outlier: 3.758A  pdb=" N   LEU A 397 " --> pdb=" O   LYS A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 424
      removed outlier: 3.646A  pdb=" N   THR A 408 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU A 413 " --> pdb=" O   GLN A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 460
      removed outlier: 3.534A  pdb=" N   THR A 450 " --> pdb=" O   GLY A 446 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   GLY A 457 " --> pdb=" O   THR A 453 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   GLU A 458 " --> pdb=" O   ILE A 454 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   LEU A 459 " --> pdb=" O   TYR A 455 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   PHE A 460 " --> pdb=" O   SER A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 464 through 486
      Proline residue:  A 484  - end of helix
    Processing helix  chain 'A' and resid 487 through 493
      removed outlier: 3.593A  pdb=" N   VAL A 491 " --> pdb=" O   LEU A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 513
      removed outlier: 4.087A  pdb=" N   LEU A 498 " --> pdb=" O   PRO A 494 " (cutoff:3.500A)
      Proline residue:  A 505  - end of helix
      removed outlier: 3.647A  pdb=" N   LEU A 513 " --> pdb=" O   GLY A 509 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49
    Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80
      removed outlier: 3.950A  pdb=" N   GLY A  84 " --> pdb=" O   GLY A  80 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 91

    264 hydrogen bonds defined for protein.
    771 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.74

  Time building geometry restraints manager: 2.34 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.83 -     1.06: 3870
        1.06 -     1.28: 604
        1.28 -     1.50: 1691
        1.50 -     1.72: 1611
        1.72 -     1.94: 41
  Bond restraints: 7817
  Sorted by residual:
  bond pdb=" CAC R75 A 601 "
       pdb=" OAG R75 A 601 "
    ideal  model  delta    sigma   weight residual
    1.326  1.397 -0.071 2.00e-02 2.50e+03 1.28e+01
  bond pdb=" CAJ R75 A 601 "
       pdb=" CAL R75 A 601 "
    ideal  model  delta    sigma   weight residual
    1.465  1.531 -0.066 2.00e-02 2.50e+03 1.10e+01
  bond pdb=" CAB R75 A 601 "
       pdb="BR2  R75 A 601 "
    ideal  model  delta    sigma   weight residual
    1.880  1.944 -0.064 2.00e-02 2.50e+03 1.03e+01
  bond pdb=" CAD R75 A 601 "
       pdb="BR1  R75 A 601 "
    ideal  model  delta    sigma   weight residual
    1.884  1.944 -0.060 2.00e-02 2.50e+03 9.05e+00
  bond pdb=" CAF R75 A 601 "
       pdb=" CAJ R75 A 601 "
    ideal  model  delta    sigma   weight residual
    1.485  1.533 -0.048 2.00e-02 2.50e+03 5.67e+00
  ... (remaining 7812 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.02: 14150
        6.02 -    12.04: 4
       12.04 -    18.06: 0
       18.06 -    24.07: 2
       24.07 -    30.09: 4
  Bond angle restraints: 14160
  Sorted by residual:
  angle pdb=" CA  ALA A 103 "
        pdb=" CB  ALA A 103 "
        pdb=" HB3 ALA A 103 "
      ideal   model   delta    sigma   weight residual
     109.00   78.91   30.09 3.00e+00 1.11e-01 1.01e+02
  angle pdb=" HB2 ALA A 103 "
        pdb=" CB  ALA A 103 "
        pdb=" HB3 ALA A 103 "
      ideal   model   delta    sigma   weight residual
     110.00   80.70   29.30 3.00e+00 1.11e-01 9.54e+01
  angle pdb=" CA  ALA A 103 "
        pdb=" CB  ALA A 103 "
        pdb=" HB1 ALA A 103 "
      ideal   model   delta    sigma   weight residual
     109.00   80.22   28.78 3.00e+00 1.11e-01 9.20e+01
  angle pdb=" HB1 ALA A 103 "
        pdb=" CB  ALA A 103 "
        pdb=" HB2 ALA A 103 "
      ideal   model   delta    sigma   weight residual
     110.00   81.39   28.61 3.00e+00 1.11e-01 9.10e+01
  angle pdb=" HB1 ALA A 103 "
        pdb=" CB  ALA A 103 "
        pdb=" HB3 ALA A 103 "
      ideal   model   delta    sigma   weight residual
     110.00  132.26  -22.26 3.00e+00 1.11e-01 5.51e+01
  ... (remaining 14155 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.89: 3491
       34.89 -    69.78: 179
       69.78 -   104.67: 12
      104.67 -   139.56: 0
      139.56 -   174.45: 1
  Dihedral angle restraints: 3683
    sinusoidal: 1980
      harmonic: 1703
  Sorted by residual:
  dihedral pdb=" CB  CYS A  49 "
           pdb=" SG  CYS A  49 "
           pdb=" SG  CYS A 116 "
           pdb=" CB  CYS A 116 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -160.16   74.16     1      1.00e+01 1.00e-02 6.98e+01
  dihedral pdb=" CAL R75 A 601 "
           pdb=" CAM R75 A 601 "
           pdb=" CAQ R75 A 601 "
           pdb=" CAR R75 A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -96.04   78.41 -174.45     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" CA  LEU A  99 "
           pdb=" C   LEU A  99 "
           pdb=" N   ASP A 100 "
           pdb=" CA  ASP A 100 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.80  -18.20     0      5.00e+00 4.00e-02 1.32e+01
  ... (remaining 3680 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 396
       0.024 -    0.048: 142
       0.048 -    0.072: 61
       0.072 -    0.096: 31
       0.096 -    0.120: 12
  Chirality restraints: 642
  Sorted by residual:
  chirality pdb=" CA  VAL A 121 "
            pdb=" N   VAL A 121 "
            pdb=" C   VAL A 121 "
            pdb=" CB  VAL A 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.61e-01
  chirality pdb=" CA  VAL A  63 "
            pdb=" N   VAL A  63 "
            pdb=" C   VAL A  63 "
            pdb=" CB  VAL A  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.61e-01
  chirality pdb=" CA  ASP A 100 "
            pdb=" N   ASP A 100 "
            pdb=" C   ASP A 100 "
            pdb=" CB  ASP A 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.60e-01
  ... (remaining 639 not shown)

  Planarity restraints: 1164
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 434 "   -0.285 9.50e-02 1.11e+02   9.51e-02 9.81e+00
        pdb=" NE  ARG A 434 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 434 "    0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 434 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 434 "   -0.003 2.00e-02 2.50e+03
        pdb="HH11 ARG A 434 "    0.003 2.00e-02 2.50e+03
        pdb="HH12 ARG A 434 "    0.001 2.00e-02 2.50e+03
        pdb="HH21 ARG A 434 "   -0.003 2.00e-02 2.50e+03
        pdb="HH22 ARG A 434 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 100 "    0.049 5.00e-02 4.00e+02   7.39e-02 8.74e+00
        pdb=" N   PRO A 101 "   -0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO A 101 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 101 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A  26 "    0.034 5.00e-02 4.00e+02   5.20e-02 4.32e+00
        pdb=" N   PRO A  27 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A  27 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A  27 "    0.029 5.00e-02 4.00e+02
  ... (remaining 1161 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.22: 604
        2.22 -     2.84: 17000
        2.84 -     3.46: 21013
        3.46 -     4.08: 28708
        4.08 -     4.70: 45605
  Nonbonded interactions: 112930
  Sorted by model distance:
  nonbonded pdb=" O   GLN A  17 "
            pdb=" HG1 THR A  21 "
     model   vdw
     1.595 2.450
  nonbonded pdb="HE21 GLN A  17 "
            pdb=" O   TRP A 224 "
     model   vdw
     1.656 2.450
  nonbonded pdb=" O   SER A 336 "
            pdb=" HG1 THR A 339 "
     model   vdw
     1.674 2.450
  nonbonded pdb=" OE1 GLU A  70 "
            pdb=" H   GLU A  70 "
     model   vdw
     1.691 2.450
  nonbonded pdb=" HH  TYR A 122 "
            pdb=" OD1 ASP A 136 "
     model   vdw
     1.703 2.450
  ... (remaining 112925 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.130
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     20.530
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   3940  Z= 0.177
  Angle     :  0.611   8.567   5391  Z= 0.297
  Chirality :  0.036   0.120    642
  Planarity :  0.007   0.125    678
  Dihedral  : 17.105 174.451   1355
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  1.55 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  : 29.12 %
    Favored  : 70.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.38), residues: 515
  helix:  1.07 (0.28), residues: 370
  sheet: -4.96 (1.17), residues: 10
  loop : -0.79 (0.55), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  96 
 HIS   0.003   0.001   HIS A 428 
 PHE   0.013   0.001   PHE A 241 
 TYR   0.010   0.001   TYR A 275 
 ARG   0.002   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18557 (  264)
  hydrogen bonds       : angle       6.91645 (  771)
  SS BOND              : bond        0.00093 (    2)
  SS BOND              : angle       0.37864 (    4)
  covalent geometry    : bond        0.00364 ( 3938)
  covalent geometry    : angle       0.61108 ( 5387)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   57 is missing expected H atoms. Skipping.
Residue THR   58 is missing expected H atoms. Skipping.
Residue SER   62 is missing expected H atoms. Skipping.
Residue VAL   63 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue THR  104 is missing expected H atoms. Skipping.
Residue THR  106 is missing expected H atoms. Skipping.
Residue SER  109 is missing expected H atoms. Skipping.
Residue LEU  321 is missing expected H atoms. Skipping.
Residue LEU  328 is missing expected H atoms. Skipping.
Residue VAL  330 is missing expected H atoms. Skipping.
Residue SER  336 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Evaluate side-chains
  103 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 101
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 0
  residues processed: 102
  average time/residue: 1.4656
  time to fit residues: 158.2972
Evaluate side-chains
  59 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.088019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.067989 restraints weight = 23475.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.2982 rms_B_bonded: 3.62
r_work: 0.2866 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.2436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3940  Z= 0.174
  Angle     :  0.642   7.243   5391  Z= 0.334
  Chirality :  0.037   0.124    642
  Planarity :  0.005   0.040    678
  Dihedral  :  8.897 156.493    555
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 31.19 %
    Favored  : 65.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.38), residues: 515
  helix:  1.69 (0.27), residues: 372
  sheet: -4.48 (1.18), residues: 10
  loop : -0.82 (0.54), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  30 
 HIS   0.002   0.001   HIS A 245 
 PHE   0.017   0.001   PHE A 362 
 TYR   0.016   0.001   TYR A 275 
 ARG   0.002   0.000   ARG A 230 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06340 (  264)
  hydrogen bonds       : angle       4.61590 (  771)
  SS BOND              : bond        0.00075 (    2)
  SS BOND              : angle       0.38153 (    4)
  covalent geometry    : bond        0.00349 ( 3938)
  covalent geometry    : angle       0.64211 ( 5387)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   57 is missing expected H atoms. Skipping.
Residue THR   58 is missing expected H atoms. Skipping.
Residue SER   62 is missing expected H atoms. Skipping.
Residue VAL   63 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue THR  104 is missing expected H atoms. Skipping.
Residue THR  106 is missing expected H atoms. Skipping.
Residue SER  109 is missing expected H atoms. Skipping.
Residue LEU  321 is missing expected H atoms. Skipping.
Residue LEU  328 is missing expected H atoms. Skipping.
Residue VAL  330 is missing expected H atoms. Skipping.
Residue SER  336 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Evaluate side-chains
  78 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.597 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 13
  outliers final: 5
  residues processed: 74
  average time/residue: 1.3861
  time to fit residues: 108.6324
Evaluate side-chains
  66 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  518 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.7988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.087011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.067005 restraints weight = 23441.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.2947 rms_B_bonded: 3.60
r_work: 0.2829 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.2976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3940  Z= 0.195
  Angle     :  0.626   5.158   5391  Z= 0.327
  Chirality :  0.038   0.138    642
  Planarity :  0.005   0.036    678
  Dihedral  :  8.671 147.901    555
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 31.44 %
    Favored  : 65.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.37), residues: 515
  helix:  1.75 (0.27), residues: 370
  sheet: -4.19 (1.35), residues: 10
  loop : -0.86 (0.52), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  30 
 HIS   0.002   0.001   HIS A 245 
 PHE   0.013   0.001   PHE A 362 
 TYR   0.017   0.001   TYR A 275 
 ARG   0.002   0.000   ARG A 230 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05736 (  264)
  hydrogen bonds       : angle       4.47121 (  771)
  SS BOND              : bond        0.00108 (    2)
  SS BOND              : angle       0.17750 (    4)
  covalent geometry    : bond        0.00418 ( 3938)
  covalent geometry    : angle       0.62578 ( 5387)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   57 is missing expected H atoms. Skipping.
Residue THR   58 is missing expected H atoms. Skipping.
Residue SER   62 is missing expected H atoms. Skipping.
Residue VAL   63 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue THR  104 is missing expected H atoms. Skipping.
Residue THR  106 is missing expected H atoms. Skipping.
Residue SER  109 is missing expected H atoms. Skipping.
Residue LEU  321 is missing expected H atoms. Skipping.
Residue LEU  328 is missing expected H atoms. Skipping.
Residue VAL  330 is missing expected H atoms. Skipping.
Residue SER  336 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Evaluate side-chains
  76 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  326 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8519 (tm-30)
  outliers start: 13
  outliers final: 8
  residues processed: 71
  average time/residue: 1.3207
  time to fit residues: 99.7232
Evaluate side-chains
  60 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ASP
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  234 MET
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  518 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0170
   chunk 39 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    0.9620

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.088390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.068609 restraints weight = 23187.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.2977 rms_B_bonded: 3.59
r_work: 0.2856 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.3267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3940  Z= 0.138
  Angle     :  0.581   4.898   5391  Z= 0.299
  Chirality :  0.036   0.150    642
  Planarity :  0.004   0.035    678
  Dihedral  :  8.544 144.296    555
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 29.12 %
    Favored  : 67.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.38), residues: 515
  helix:  1.88 (0.27), residues: 371
  sheet: -3.94 (1.42), residues: 10
  loop : -0.92 (0.53), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP A 285 
 HIS   0.002   0.000   HIS A 245 
 PHE   0.011   0.001   PHE A 360 
 TYR   0.015   0.001   TYR A 275 
 ARG   0.001   0.000   ARG A 203 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05113 (  264)
  hydrogen bonds       : angle       4.19336 (  771)
  SS BOND              : bond        0.00084 (    2)
  SS BOND              : angle       0.27950 (    4)
  covalent geometry    : bond        0.00301 ( 3938)
  covalent geometry    : angle       0.58082 ( 5387)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   57 is missing expected H atoms. Skipping.
Residue THR   58 is missing expected H atoms. Skipping.
Residue SER   62 is missing expected H atoms. Skipping.
Residue VAL   63 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue THR  104 is missing expected H atoms. Skipping.
Residue THR  106 is missing expected H atoms. Skipping.
Residue SER  109 is missing expected H atoms. Skipping.
Residue LEU  321 is missing expected H atoms. Skipping.
Residue LEU  328 is missing expected H atoms. Skipping.
Residue VAL  330 is missing expected H atoms. Skipping.
Residue SER  336 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Evaluate side-chains
  72 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 57
  time to evaluate  : 0.573 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 VAL cc_start: 0.8410 (OUTLIER) cc_final: 0.8176 (t)
REVERT: A  281 GLU cc_start: 0.7829 (tp30) cc_final: 0.7388 (pm20)
  outliers start: 15
  outliers final: 9
  residues processed: 68
  average time/residue: 1.4690
  time to fit residues: 105.8658
Evaluate side-chains
  66 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ASP
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  222 MET
Chi-restraints excluded: chain A residue  234 MET
Chi-restraints excluded: chain A residue  282 SER
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  518 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   overall best weight:    1.2584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.088164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.068098 restraints weight = 22956.318|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 3.61
r_work: 0.2848 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.3488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3940  Z= 0.155
  Angle     :  0.585   4.615   5391  Z= 0.305
  Chirality :  0.036   0.167    642
  Planarity :  0.004   0.033    678
  Dihedral  :  8.469 141.569    555
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 29.64 %
    Favored  : 67.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.38), residues: 515
  helix:  1.99 (0.27), residues: 371
  sheet: -3.85 (1.47), residues: 10
  loop : -0.91 (0.54), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 285 
 HIS   0.002   0.000   HIS A 245 
 PHE   0.012   0.001   PHE A 208 
 TYR   0.016   0.001   TYR A 275 
 ARG   0.002   0.000   ARG A 487 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04944 (  264)
  hydrogen bonds       : angle       4.16280 (  771)
  SS BOND              : bond        0.00062 (    2)
  SS BOND              : angle       0.14481 (    4)
  covalent geometry    : bond        0.00339 ( 3938)
  covalent geometry    : angle       0.58477 ( 5387)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   57 is missing expected H atoms. Skipping.
Residue THR   58 is missing expected H atoms. Skipping.
Residue SER   62 is missing expected H atoms. Skipping.
Residue VAL   63 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue THR  104 is missing expected H atoms. Skipping.
Residue THR  106 is missing expected H atoms. Skipping.
Residue SER  109 is missing expected H atoms. Skipping.
Residue LEU  321 is missing expected H atoms. Skipping.
Residue LEU  328 is missing expected H atoms. Skipping.
Residue VAL  330 is missing expected H atoms. Skipping.
Residue SER  336 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Evaluate side-chains
  68 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.569 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  223 GLU cc_start: 0.7520 (tt0) cc_final: 0.7283 (tt0)
REVERT: A  281 GLU cc_start: 0.7867 (tp30) cc_final: 0.7361 (pm20)
REVERT: A  326 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8655 (tm-30)
REVERT: A  370 ASP cc_start: 0.6918 (OUTLIER) cc_final: 0.6430 (p0)
  outliers start: 12
  outliers final: 9
  residues processed: 65
  average time/residue: 1.8858
  time to fit residues: 131.1968
Evaluate side-chains
  64 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 2.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ASP
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   32 CYS
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  234 MET
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  370 ASP
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  518 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 5 optimal weight:    0.4980
   chunk 12 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 50 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.088981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.068872 restraints weight = 22787.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.2983 rms_B_bonded: 3.63
r_work: 0.2866 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.3646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3940  Z= 0.124
  Angle     :  0.563   4.619   5391  Z= 0.288
  Chirality :  0.035   0.123    642
  Planarity :  0.005   0.056    678
  Dihedral  :  8.316 138.790    555
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 29.64 %
    Favored  : 67.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.39), residues: 515
  helix:  2.07 (0.28), residues: 373
  sheet: -3.65 (1.54), residues: 10
  loop : -0.98 (0.55), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP A 285 
 HIS   0.002   0.000   HIS A 245 
 PHE   0.011   0.001   PHE A 208 
 TYR   0.014   0.001   TYR A 275 
 ARG   0.007   0.000   ARG A 230 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04560 (  264)
  hydrogen bonds       : angle       4.00115 (  771)
  SS BOND              : bond        0.00075 (    2)
  SS BOND              : angle       0.24112 (    4)
  covalent geometry    : bond        0.00275 ( 3938)
  covalent geometry    : angle       0.56352 ( 5387)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   57 is missing expected H atoms. Skipping.
Residue THR   58 is missing expected H atoms. Skipping.
Residue SER   62 is missing expected H atoms. Skipping.
Residue VAL   63 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue THR  104 is missing expected H atoms. Skipping.
Residue THR  106 is missing expected H atoms. Skipping.
Residue SER  109 is missing expected H atoms. Skipping.
Residue LEU  321 is missing expected H atoms. Skipping.
Residue LEU  328 is missing expected H atoms. Skipping.
Residue VAL  330 is missing expected H atoms. Skipping.
Residue SER  336 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Evaluate side-chains
  66 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.609 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 GLU cc_start: 0.7543 (tm-30) cc_final: 0.6940 (tm-30)
REVERT: A  223 GLU cc_start: 0.7440 (tt0) cc_final: 0.7234 (tt0)
REVERT: A  281 GLU cc_start: 0.7903 (tp30) cc_final: 0.7315 (pm20)
  outliers start: 11
  outliers final: 9
  residues processed: 65
  average time/residue: 1.3764
  time to fit residues: 94.8150
Evaluate side-chains
  65 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.598 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ASP
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  234 MET
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  370 ASP
Chi-restraints excluded: chain A residue  518 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0570
   overall best weight:    0.9300

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.088551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.068479 restraints weight = 23022.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 3.60
r_work: 0.2864 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.3753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3940  Z= 0.134
  Angle     :  0.581   5.716   5391  Z= 0.297
  Chirality :  0.035   0.121    642
  Planarity :  0.004   0.033    678
  Dihedral  :  8.191 137.114    555
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 29.12 %
    Favored  : 67.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.39), residues: 515
  helix:  2.15 (0.28), residues: 371
  sheet: -3.62 (1.60), residues: 10
  loop : -0.87 (0.55), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP A 285 
 HIS   0.002   0.000   HIS A 245 
 PHE   0.011   0.001   PHE A 208 
 TYR   0.015   0.001   TYR A 275 
 ARG   0.002   0.000   ARG A 203 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04476 (  264)
  hydrogen bonds       : angle       3.96851 (  771)
  SS BOND              : bond        0.00090 (    2)
  SS BOND              : angle       0.22629 (    4)
  covalent geometry    : bond        0.00301 ( 3938)
  covalent geometry    : angle       0.58165 ( 5387)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   57 is missing expected H atoms. Skipping.
Residue THR   58 is missing expected H atoms. Skipping.
Residue SER   62 is missing expected H atoms. Skipping.
Residue VAL   63 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue THR  104 is missing expected H atoms. Skipping.
Residue THR  106 is missing expected H atoms. Skipping.
Residue SER  109 is missing expected H atoms. Skipping.
Residue LEU  321 is missing expected H atoms. Skipping.
Residue LEU  328 is missing expected H atoms. Skipping.
Residue VAL  330 is missing expected H atoms. Skipping.
Residue SER  336 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Evaluate side-chains
  68 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 55
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6857 (tm-30)
  outliers start: 13
  outliers final: 10
  residues processed: 64
  average time/residue: 1.8382
  time to fit residues: 124.4302
Evaluate side-chains
  65 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 54
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ASP
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   32 CYS
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  370 ASP
Chi-restraints excluded: chain A residue  518 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 41 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0470
   chunk 34 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 4 optimal weight:    4.9990
   chunk 39 optimal weight:    0.6980
   chunk 6 optimal weight:    7.9990
   chunk 7 optimal weight:    0.5980
   chunk 50 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   overall best weight:    0.5878

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.089397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.069607 restraints weight = 23040.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.2996 rms_B_bonded: 3.59
r_work: 0.2879 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.3863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   3940  Z= 0.118
  Angle     :  0.570   6.492   5391  Z= 0.289
  Chirality :  0.035   0.123    642
  Planarity :  0.004   0.035    678
  Dihedral  :  8.096 135.151    555
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 29.38 %
    Favored  : 67.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.39), residues: 515
  helix:  2.23 (0.28), residues: 373
  sheet: -3.49 (1.61), residues: 10
  loop : -1.05 (0.55), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP A 285 
 HIS   0.001   0.000   HIS A 245 
 PHE   0.010   0.001   PHE A 208 
 TYR   0.014   0.001   TYR A 275 
 ARG   0.001   0.000   ARG A 284 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04248 (  264)
  hydrogen bonds       : angle       3.87357 (  771)
  SS BOND              : bond        0.00073 (    2)
  SS BOND              : angle       0.30405 (    4)
  covalent geometry    : bond        0.00263 ( 3938)
  covalent geometry    : angle       0.57004 ( 5387)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   57 is missing expected H atoms. Skipping.
Residue THR   58 is missing expected H atoms. Skipping.
Residue SER   62 is missing expected H atoms. Skipping.
Residue VAL   63 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue THR  104 is missing expected H atoms. Skipping.
Residue THR  106 is missing expected H atoms. Skipping.
Residue SER  109 is missing expected H atoms. Skipping.
Residue LEU  321 is missing expected H atoms. Skipping.
Residue LEU  328 is missing expected H atoms. Skipping.
Residue VAL  330 is missing expected H atoms. Skipping.
Residue SER  336 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Evaluate side-chains
  72 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 59
  time to evaluate  : 0.527 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  326 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8435 (pp20)
REVERT: A  327 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8557 (mm-30)
  outliers start: 13
  outliers final: 11
  residues processed: 68
  average time/residue: 1.4457
  time to fit residues: 104.1674
Evaluate side-chains
  63 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 52
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ASP
Chi-restraints excluded: chain A residue   32 CYS
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  370 ASP
Chi-restraints excluded: chain A residue  518 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 33 optimal weight:    0.1980
   chunk 21 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0980
   chunk 46 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0170
   chunk 27 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.4018

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.089741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.069903 restraints weight = 23084.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.3011 rms_B_bonded: 3.59
r_work: 0.2894 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.4043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   3940  Z= 0.114
  Angle     :  0.563   6.615   5391  Z= 0.285
  Chirality :  0.035   0.122    642
  Planarity :  0.005   0.055    678
  Dihedral  :  7.992 133.263    555
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 29.90 %
    Favored  : 66.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.04 (0.39), residues: 515
  helix:  2.25 (0.28), residues: 373
  sheet: -3.22 (1.61), residues: 10
  loop : -0.97 (0.56), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 285 
 HIS   0.001   0.000   HIS A 245 
 PHE   0.010   0.001   PHE A 360 
 TYR   0.013   0.001   TYR A 275 
 ARG   0.008   0.000   ARG A 230 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04044 (  264)
  hydrogen bonds       : angle       3.81573 (  771)
  SS BOND              : bond        0.00073 (    2)
  SS BOND              : angle       0.35857 (    4)
  covalent geometry    : bond        0.00258 ( 3938)
  covalent geometry    : angle       0.56289 ( 5387)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   57 is missing expected H atoms. Skipping.
Residue THR   58 is missing expected H atoms. Skipping.
Residue SER   62 is missing expected H atoms. Skipping.
Residue VAL   63 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue THR  104 is missing expected H atoms. Skipping.
Residue THR  106 is missing expected H atoms. Skipping.
Residue SER  109 is missing expected H atoms. Skipping.
Residue LEU  321 is missing expected H atoms. Skipping.
Residue LEU  328 is missing expected H atoms. Skipping.
Residue VAL  330 is missing expected H atoms. Skipping.
Residue SER  336 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Evaluate side-chains
  70 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8595 (mm-30)
  outliers start: 13
  outliers final: 8
  residues processed: 66
  average time/residue: 1.4153
  time to fit residues: 98.9400
Evaluate side-chains
  68 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ASP
Chi-restraints excluded: chain A residue   32 CYS
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  387 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 44 optimal weight:    0.7980
   chunk 50 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 29 optimal weight:    4.9990
   chunk 6 optimal weight:    0.5980
   chunk 3 optimal weight:    2.9990
   chunk 10 optimal weight:    9.9990
   chunk 1 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.088844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.069411 restraints weight = 22715.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 3.51
r_work: 0.2879 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.4151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   3940  Z= 0.127
  Angle     :  0.580   6.037   5391  Z= 0.292
  Chirality :  0.035   0.120    642
  Planarity :  0.004   0.044    678
  Dihedral  :  7.914 132.563    555
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 31.70 %
    Favored  : 66.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.10 (0.39), residues: 515
  helix:  2.30 (0.28), residues: 371
  sheet: -3.08 (1.64), residues: 10
  loop : -0.92 (0.55), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 285 
 HIS   0.001   0.000   HIS A 245 
 PHE   0.010   0.001   PHE A 360 
 TYR   0.014   0.001   TYR A 275 
 ARG   0.005   0.000   ARG A 230 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04062 (  264)
  hydrogen bonds       : angle       3.83870 (  771)
  SS BOND              : bond        0.00073 (    2)
  SS BOND              : angle       0.29643 (    4)
  covalent geometry    : bond        0.00292 ( 3938)
  covalent geometry    : angle       0.58063 ( 5387)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   57 is missing expected H atoms. Skipping.
Residue THR   58 is missing expected H atoms. Skipping.
Residue SER   62 is missing expected H atoms. Skipping.
Residue VAL   63 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue THR  104 is missing expected H atoms. Skipping.
Residue THR  106 is missing expected H atoms. Skipping.
Residue SER  109 is missing expected H atoms. Skipping.
Residue LEU  321 is missing expected H atoms. Skipping.
Residue LEU  328 is missing expected H atoms. Skipping.
Residue VAL  330 is missing expected H atoms. Skipping.
Residue SER  336 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Evaluate side-chains
  70 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.532 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8690 (mm-30)
REVERT: A  114 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7203 (tp30)
REVERT: A  257 ASP cc_start: 0.7858 (t0) cc_final: 0.7539 (t0)
REVERT: A  281 GLU cc_start: 0.8130 (tp30) cc_final: 0.7581 (mp0)
REVERT: A  326 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8689 (pp20)
REVERT: A  327 GLU cc_start: 0.9294 (mm-30) cc_final: 0.8718 (mm-30)
  outliers start: 8
  outliers final: 6
  residues processed: 67
  average time/residue: 1.4271
  time to fit residues: 101.1777
Evaluate side-chains
  64 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ASP
Chi-restraints excluded: chain A residue   32 CYS
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  275 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 16 optimal weight:    0.2980
   chunk 35 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 10 optimal weight:    0.4980
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.088930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.069309 restraints weight = 22575.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.2999 rms_B_bonded: 3.50
r_work: 0.2880 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.4204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   3940  Z= 0.129
  Angle     :  0.576   6.068   5391  Z= 0.293
  Chirality :  0.035   0.120    642
  Planarity :  0.005   0.094    678
  Dihedral  :  7.884 132.012    555
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 30.93 %
    Favored  : 65.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.15 (0.39), residues: 515
  helix:  2.35 (0.28), residues: 371
  sheet: -2.92 (1.70), residues: 10
  loop : -0.94 (0.55), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  30 
 HIS   0.001   0.000   HIS A 245 
 PHE   0.010   0.001   PHE A 360 
 TYR   0.014   0.002   TYR A 275 
 ARG   0.017   0.001   ARG A 230 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04107 (  264)
  hydrogen bonds       : angle       3.84268 (  771)
  SS BOND              : bond        0.00076 (    2)
  SS BOND              : angle       0.27231 (    4)
  covalent geometry    : bond        0.00294 ( 3938)
  covalent geometry    : angle       0.57580 ( 5387)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5078.80 seconds
wall clock time: 89 minutes 26.63 seconds (5366.63 seconds total)